Sequence-subtype association of multi-drug-resistant diarrheagenic Escherichia coli
Abstract
Background and Objectives: Multi-drug-resistant pathogens pose a significant threat as they can rapidly spread, leading to severe healthcare-associated invasive infections. In developing countries, diarrheagenic Escherichia coli (DEC) is a major bacterial pathogen responsible for causing diarrhea. However, the outbreak of resistant strains has made the treatment of DEC infections much more challenging. This study aimed to investigate the relationship between antibiotic resistance genes and other virulence categories in E. coli strains that cause diarrhea, particularly DEC.
Materials and Methods: The phylogenetic grouping was defined using PCR and multi-locus sequence type (MLST) methods.
Results: Among the isolates analyzed, 14 were identified as resistant and were classified into eight distinct sequence types: ST3, ST53, ST77, ST483, ST512, ST636, ST833, and ST774, indicating genetic diversity among the resistant strains. Certain sequence types, notably ST512 and ST636, were found to be associated with multiple antibiotic resistance in DEC. Regarding antibiotic susceptibility, strains showed the highest resistance to amoxicillin, suggesting that this antibiotic may not be effective in treating DEC infections. On the other hand, the isolates demonstrated susceptibility to amikacin and chloramphenicol, implying that these antibiotics could be more suitable treatment options for DEC infections.
Conclusion: The findings underscore the importance of promptly identifying antibiotic resistance patterns and their correlation with specific pathogenic virulence categories, as this knowledge can aid in selecting the most appropriate antibiotics for treating DEC infections. Considering the antibiotic resistance profiles and associated resistance genes is crucial in managing and containing diarrheal outbreaks and in selecting effective antibiotic therapies for DEC infections.
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27. Harada H, Fujimori Y, Gomi R, Ahsan MN, Fujii S, Sakai A, et al. Pathotyping of Escherichia coli isolated from community toilet wastewater and stored drinking water in a slum in Bangladesh. Lett Appl Microbiol 2018; 66: 542-548.
28. Eybpoosh S, Mostaan S, Gouya MM, Masoumi-Asl H, Owlia P, Eshrati B, et al. Frequency of five Escherichia coli pathotypes in Iranian adults and children with acute diarrhea. PLoS One 2021; 16(2): e0245470.
29. Delannoy S, Mariani-Kurkdjian P, Bonacorsi S, Liguori S, Ison SA, Fach P. Draft genome sequences of human-pathogenic Escherichia coli O26:H11 strains carrying the stx2 gene only and circulating in France. Genome Announc 2015; 3(4): e00852-15.
30. Duriez P, Clermont O, Bonacorsi S, Bingen E, Chaventre A, Elion J, et al. Commensal Escherichia coli isolates are phylogenetically distributed among geographically distinct human populations. Microbiology (Reading) 2001; 147: 1671-1676.
31. Blyton MD, Cornall SJ, Kennedy K, Colligon P, Gordon DM. Sex-dependent competitive dominance of phylogenetic group B2 Escherichia coli strains within human hosts. Environ Microbiol Rep 2014; 6: 605-610.
32. Spano LC, da Cunha KF, Monfardini MV, de Cássia Bergamaschi Fonseca R, Scaletsky ICA. High prevalence of diarrheagenic Escherichia coli carrying toxin-encoding genes isolated from children and adults in southeastern Brazil. BMC Infect Dis 2017; 17: 773.
33. Jarocki VM, Reid CJ, Chapman TA, Djordjevic SP. Escherichia coli ST302: Genomic analysis of virulence potential and antimicrobial resistance mediated by mobile genetic elements. Front Microbiol 2020; 10: 3098.
34. Shakya P, Barrett P, Diwan V, Marothi Y, Shah H, Chhari N, et al. Antibiotic resistance among Escherichia coli isolates from stool samples of children aged 3 to 14 years from Ujjain, India. BMC Infect Dis 2013; 13: 477.
35. Magiorakos AP, Srinivasan A, Carey RB, Carmeli Y, Falagas ME, Giske CG, et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect 2012; 18: 268-281.
36. Yu F, Chen X, Zheng S, Han D, Wang Y, Wang R, et al. Prevalence and genetic diversity of human diarrheagenic Escherichia coli isolates by Multilocus sequence typing. Int J Infect Dis 2018; 67: 7-13.
37. Aworh MK, Kwaga JKP, Hendriksen RS, Okolocha EC, Thakur S. Genetic relatedness of multidrug resistant Escherichia coli isolated from humans, chickens and poultry environments. Antimicrob Resist Infect Control 2021; 10: 58.
2. Clermont O, Christenson JK, Denamur E, Gordon DM. The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ Microbiol Rep 2013; 5: 58-65.
3. Johnson JR, Russo TA. Extraintestinal pathogenic Escherichia coli: "the other bad E. coli". J Lab Clin Med 2002; 139: 155-162.
4. Croxen MA, Finlay BB. Molecular mechanisms of Escherichia coli pathogenicity. Nat Rev Microbiol 2010; 8: 26-38.
5. Cooke NM, Smith SG, Kelleher M, Rogers TR. Major differences exist in frequencies of virulence factors and multidrug resistance between community and nosocomial Escherichia coli bloodstream isolates. J Clin Microbiol 2010; 48: 1099-1104.
6. Boerlin P, Travis R, Gyles CL, Reid-Smith R, Janecko N, Lim H, et al. Antimicrobial resistance and virulence genes of Escherichia coli isolates from swine in Ontario. Appl Environ Microbiol 2005; 71: 6753-6761.
7. Wang X-M, Jiang H-X, Liao X-P, Liu J-H, Zhang W-J, Zhang H, et al. Antimicrobial resistance, virulence genes, and phylogenetic background in Escherichia coli isolates from diseased pigs. FEMS Microbiol Lett 2010; 306: 15-21.
8. Maiden MC. Multilocus sequence typing of bacteria. Annu Rev Microbiol 2006; 60: 561-588.
9. Feil EJ. Small change: keeping pace with microevolution. Nat Rev Microbiol 2004; 2: 483-495.
10. Jaureguy F, Landraud L, Passet V, Diancourt L, Frapy E, Guigon G, et al. Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains. BMC Genomics 2008; 9: 560.
11. Chaudhuri RR, Henderson IR. The evolution of the Escherichia coli phylogeny. Infect Genet Evol 2012; 12: 214-226.
12. Clermont O, Gordon D, Denamur E. Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes. Microbiology (Reading) 2015; 161: 980-988.
13. Rouli L, Merhej V, Fournier P-E, Raoult D. The bacterial pangenome as a new tool for analyzing pathogenic bacteria. New Microbes New Infect 2015; 7: 72-85.
14. McNally A, Oren Y, Kelly D, Pascoe B, Dunn S, Sreecharan T, et al. Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations. PLoS Genet 2016; 12(9): e1006280.
15. Hien BT, Scheutz F, Cam PD, Serichantalergs O, Huong TT, Thu TM, et al. Diarrheagenic Escherichia coli and Shigella strains isolated from children in a hospital case-control study in Hanoi, Vietnam. J Clin Microbiol 2008; 46: 996-1004.
16. Thakur N, Jain S, Changotra H, Shrivastava R, Kumar Y, Grover N, et al. Molecular characterization of diarrheagenic Escherichia coli pathotypes: Association of virulent genes, serogroups, and antibiotic resistance among moderate-to-severe diarrhea patients. J Clin Lab Anal 2018; 32(5): e22388.
17. Eklund M, Scheutz F, Siitonen A. Clinical isolates of non-O157 Shiga toxin-producing Escherichia coli: serotypes, virulence characteristics, and molecular profiles of strains of the same serotype. J Clin Microbiol 2001; 39: 2829-2834.
18. Clermont O, Bonacorsi S, Bingen E. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl Environ Microbiol 2000; 66: 4555-4558.
19. Sánchez S, Llorente MT, Echeita MA, Herrera-León S. Development of three multiplex PCR assays targeting the 21 most clinically relevant serogroups associated with Shiga toxin-producing E. coli infection in humans. PLoS One 2015; 10(1): e0117660.
20. DebRoy C, Roberts E, Fratamico PM. Detection of O antigens in Escherichia coli. Anim Health Res Rev 2011; 12: 169-185.
21. Bardbari AM, Arabestani MR, Karami M, Keramat F, Aghazadeh H, Alikhani MY, et al. Highly synergistic activity of melittin with imipenem and colistin in biofilm inhibition against multidrug-resistant strong biofilm producer strains of Acinetobacter baumannii. Eur J Clin Microbiol Infect Dis 2018; 37: 443-454.
22. Ludwig JB, Shi X, Shridhar PB, Roberts EL, DebRoy C, Phebus RK, et al. Multiplex PCR assays for the detection of one hundred and thirty seven serogroups of Shiga toxin-producing Escherichia coli associated with cattle. Front Cell Infect Microbiol 2020; 10: 378.
23. Alikhani MY, Hashemi SH, Aslani MM, Farajnia S. Prevalence and antibiotic resistance patterns of diarrheagenic Escherichia coli isolated from adolescents and adults in Hamedan, Western Iran. Iran J Microbiol 2013; 5: 42-47.
24. Canizalez-Roman A, Flores-Villaseñor HM, Gonzalez-Nuñez E, Velazquez-Roman J, Vidal JE, Muro-Amador S, et al. Surveillance of diarrheagenic Escherichia coli strains isolated from diarrhea cases from children, adults and elderly at northwest of Mexico. Front Microbiol 2016; 7: 1924.
25. Khan A, Yamasaki S, Sato T, Ramamurthy T, Pal A, Datta S, et al. Prevalence and genetic profiling of virulence determinants of non-O157 Shiga toxin-producing Escherichia coli isolated from cattle, beef, and humans, Calcutta, India. Emerg Infect Dis 2002; 8: 54-62.
26. Flaherty KE, Grembi JA, Ramachandran VV, Haque F, Khatun S, Rahman M, et al. High-throughput low-cost nl-qPCR for enteropathogen detection: A proof-of-concept among hospitalized patients in Bangladesh. PLoS One 2021; 16(10): e0257708.
27. Harada H, Fujimori Y, Gomi R, Ahsan MN, Fujii S, Sakai A, et al. Pathotyping of Escherichia coli isolated from community toilet wastewater and stored drinking water in a slum in Bangladesh. Lett Appl Microbiol 2018; 66: 542-548.
28. Eybpoosh S, Mostaan S, Gouya MM, Masoumi-Asl H, Owlia P, Eshrati B, et al. Frequency of five Escherichia coli pathotypes in Iranian adults and children with acute diarrhea. PLoS One 2021; 16(2): e0245470.
29. Delannoy S, Mariani-Kurkdjian P, Bonacorsi S, Liguori S, Ison SA, Fach P. Draft genome sequences of human-pathogenic Escherichia coli O26:H11 strains carrying the stx2 gene only and circulating in France. Genome Announc 2015; 3(4): e00852-15.
30. Duriez P, Clermont O, Bonacorsi S, Bingen E, Chaventre A, Elion J, et al. Commensal Escherichia coli isolates are phylogenetically distributed among geographically distinct human populations. Microbiology (Reading) 2001; 147: 1671-1676.
31. Blyton MD, Cornall SJ, Kennedy K, Colligon P, Gordon DM. Sex-dependent competitive dominance of phylogenetic group B2 Escherichia coli strains within human hosts. Environ Microbiol Rep 2014; 6: 605-610.
32. Spano LC, da Cunha KF, Monfardini MV, de Cássia Bergamaschi Fonseca R, Scaletsky ICA. High prevalence of diarrheagenic Escherichia coli carrying toxin-encoding genes isolated from children and adults in southeastern Brazil. BMC Infect Dis 2017; 17: 773.
33. Jarocki VM, Reid CJ, Chapman TA, Djordjevic SP. Escherichia coli ST302: Genomic analysis of virulence potential and antimicrobial resistance mediated by mobile genetic elements. Front Microbiol 2020; 10: 3098.
34. Shakya P, Barrett P, Diwan V, Marothi Y, Shah H, Chhari N, et al. Antibiotic resistance among Escherichia coli isolates from stool samples of children aged 3 to 14 years from Ujjain, India. BMC Infect Dis 2013; 13: 477.
35. Magiorakos AP, Srinivasan A, Carey RB, Carmeli Y, Falagas ME, Giske CG, et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect 2012; 18: 268-281.
36. Yu F, Chen X, Zheng S, Han D, Wang Y, Wang R, et al. Prevalence and genetic diversity of human diarrheagenic Escherichia coli isolates by Multilocus sequence typing. Int J Infect Dis 2018; 67: 7-13.
37. Aworh MK, Kwaga JKP, Hendriksen RS, Okolocha EC, Thakur S. Genetic relatedness of multidrug resistant Escherichia coli isolated from humans, chickens and poultry environments. Antimicrob Resist Infect Control 2021; 10: 58.
| Files | ||
| Issue | Vol 16 No 2 (2024) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijm.v16i2.15350 | |
| Keywords | ||
| Escherichia coli; Multilocus sequence typing; Multidrug resistant; β-lactams; Virulence factors | ||
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How to Cite
1.
Farzi N, Pourramezan Z, Akhavan Attar F, Mostaan S, Oloomi M. Sequence-subtype association of multi-drug-resistant diarrheagenic Escherichia coli. Iran J Microbiol. 2024;16(2):176-186.
